version update for LRSDAY: v1.3.1 -> v1.4.0

yjx1217 · Mar 21, 2019 · 8f05225 · 8f05225
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,6 +7,15 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ## [Unreleased]
 
+## [1.4.0] - 2019-03-21
+### Changed
+- Supports for multi-round assembly polishing using both long and short reads.
+- Setting adjustment for long-read filtering and downsampling.
+- Software version updates for a number of dependencies. 
+### Fixed
+- Compatibility issues due to recent version updates of conda an bioconda.
+- Typos in the installation script.
+
 ## [1.3.1] - 2019-01-22
 ### Added
 - A script for generated demultiplexed fastq reads based on nanopore's guppy demultiplexing summary file.

diff --git a/Example_Outputs/SK1.assembly.final.fa.gz b/Example_Outputs/SK1.assembly.final.fa.gz
diff --git a/Example_Outputs/SK1.assembly.final.filter.mummer2vcf.INDEL.vcf.gz b/Example_Outputs/SK1.assembly.final.filter.mummer2vcf.INDEL.vcf.gz
diff --git a/Example_Outputs/SK1.assembly.final.filter.mummer2vcf.SNP.vcf.gz b/Example_Outputs/SK1.assembly.final.filter.mummer2vcf.SNP.vcf.gz
diff --git a/Example_Outputs/SK1.assembly.final.filter.pdf b/Example_Outputs/SK1.assembly.final.filter.pdf
diff --git a/Example_Outputs/SK1.assembly.final.stats.txt b/Example_Outputs/SK1.assembly.final.stats.txt
@@ -1,8 +1,8 @@
 total sequence count: 34
-total sequence length: 12448004
+total sequence length: 12448003
 min sequence length: 1248
 max sequence length: 1480301
-mean sequence length: 366117.76
+mean sequence length: 366117.74
 median sequence length: 60826.50
 N50: 923676
 L50: 6

diff --git a/Example_Outputs/SK1.final.cds.fa.gz b/Example_Outputs/SK1.final.cds.fa.gz
diff --git a/Example_Outputs/SK1.final.gff3.gz b/Example_Outputs/SK1.final.gff3.gz
diff --git a/Example_Outputs/SK1.final.manual_check.list b/Example_Outputs/SK1.final.manual_check.list
@@ -218,25 +218,22 @@ SK1_G0056290|SK1_G0056290.mRNA.1	unexpected start & end codons based on standard
 SK1_G0057300|SK1_G0057300.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;incorrect CDS length
 SK1_G0057390|SK1_G0057390.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
 SK1_G0057410|SK1_G0057410.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0057460|SK1_G0057460.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0057480|SK1_G0057480.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
+SK1_G0057470|SK1_G0057470.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
+SK1_G0057490|SK1_G0057490.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
 SK1_G0057500|SK1_G0057500.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0057510|SK1_G0057510.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0057570|SK1_G0057570.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0057590|SK1_G0057590.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0057750|SK1_G0057750.mRNA.1	incorrect CDS length
-SK1_G0057780|SK1_G0057780.mRNA.1	incorrect CDS length
-SK1_G0057800|SK1_G0057800.mRNA.1	incorrect CDS length
+SK1_G0057560|SK1_G0057560.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
+SK1_G0057580|SK1_G0057580.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
+SK1_G0057770|SK1_G0057770.mRNA.1	incorrect CDS length
+SK1_G0057950|SK1_G0057950.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
 SK1_G0057960|SK1_G0057960.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
 SK1_G0057970|SK1_G0057970.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0057980|SK1_G0057980.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
+SK1_G0058000|SK1_G0058000.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
 SK1_G0058010|SK1_G0058010.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
 SK1_G0058020|SK1_G0058020.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0058030|SK1_G0058030.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0058070|SK1_G0058070.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0058160|SK1_G0058160.mRNA.1	unexpected start codon based on standard genentic code;your selected code table is 1;incorrect CDS length
-SK1_G0058260|SK1_G0058260.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
-SK1_G0058280|SK1_G0058280.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
+SK1_G0058060|SK1_G0058060.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
+SK1_G0058150|SK1_G0058150.mRNA.1	unexpected start codon based on standard genentic code;your selected code table is 1;incorrect CDS length
+SK1_G0058250|SK1_G0058250.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
+SK1_G0058270|SK1_G0058270.mRNA.1	unexpected start & end codons based on standard genentic code;your selected code table is 1;internal stop codon(s)
 cox2|cox2.mRNA.1	unexpected stop codon based on standard genentic code;your selected code table is 3;incorrect CDS length
 orf474|orf474.mRNA.1	unexpected start codon based on standard genentic code;your selected code table is 3;incorrect CDS length
 orf90|orf90.mRNA.1	unexpected start codon based on standard genentic code;your selected code table is 3

diff --git a/Example_Outputs/SK1.final.pep.fa.gz b/Example_Outputs/SK1.final.pep.fa.gz
diff --git a/Example_Outputs/SK1.final.trimmed_cds.fa.gz b/Example_Outputs/SK1.final.trimmed_cds.fa.gz
diff --git a/Manual.pdf b/Manual.pdf
diff --git a/Project_Template/00.Long_Reads/LRSDAY.00.Long_Reads_Preprocessing.sh b/Project_Template/00.Long_Reads/LRSDAY.00.Long_Reads_Preprocessing.sh
@@ -12,27 +12,31 @@ reads="./../00.Long_Reads/YGL3210.fq.gz" # The file path of the long reads file
 reads_type="nanopore-raw" # The long reads data type: "pacbio-raw" or "pacbio-corrected" or "nanopore-raw" or "nanopore-corrected".
 run_filtering="yes" # Whether to filter the reads: "yes" or "no". Default = "yes".
 genome_size="12500000" # The haploid genome size (in bp) of sequenced organism. Default = "12500000" (i.e. 12.5 Mb for the budding yeast S. cereviaie genome). This is used to calculate targeted sequencing coverage after read filtering (see below). 
-post_filtering_coverage="30" # Targeted sequencing coverage after read filtering. Default = "30" (i.e. 30x coverage).
+post_filtering_coverage="40" # Targeted sequencing coverage after read filtering. Default = "40" (i.e. 40x coverage).
 threads=1 # The number of threads to use. Default = "1".
 
 #######################################
 # process the pipeline
 
-filtlong_target_bases=$(($genome_size * $post_filtering_coverage))
-echo ""
-echo "genome_size=$genome_size, post_filtering_coverage=$post_filtering_coverage, filtlong_target_bases=$filtlong_target_bases"
-echo ""
 if [[ "$reads_type" == "nanopore-raw" || "$reads_type" == "nanopore-corrected" ]]
 then
     $porechop_dir/porechop -i $reads -o $prefix.porechop.fastq.gz --discard_middle --threads $threads > $prefix.porechop.summary.txt
     if [[ "$run_filtering" == "yes" ]]
     then
-	$filtlong_dir/filtlong --min_length 1000 --keep_percent 90 --target_bases $filtlong_target_bases $prefix.porechop.fastq.gz | gzip > $prefix.filtlong.fastq.gz
+	filtlong_target_bases=$(($genome_size * $post_filtering_coverage))
+	echo ""
+	echo "genome_size=$genome_size, post_filtering_coverage=$post_filtering_coverage, filtlong_target_bases=$filtlong_target_bases"
+	echo ""
+	$filtlong_dir/filtlong --min_length 1000 --mean_q_weight 10 --target_bases $filtlong_target_bases $prefix.porechop.fastq.gz | gzip > $prefix.filtlong.fastq.gz
     fi
 else
     if [[ "$run_filtering" == "yes" ]]
     then
-	$filtlong_dir/filtlong --min_length 1000 --keep_percent 90 --target_bases $filtlong_target_bases $reads | gzip > $prefix.filtlong.fastq.gz
+	filtlong_target_bases=$(($genome_size * $post_filtering_coverage))
+	echo ""
+	echo "genome_size=$genome_size, post_filtering_coverage=$post_filtering_coverage, filtlong_target_bases=$filtlong_target_bases"
+	echo ""
+	$filtlong_dir/filtlong --min_length 1000 --mean_q_weight 10 --target_bases $filtlong_target_bases $reads | gzip > $prefix.filtlong.fastq.gz
     fi
 fi
 

diff --git a/Project_Template/00.Long_Reads/LRSDAY.00.PacBio.RSII_bax2bam.sh b/Project_Template/00.Long_Reads/LRSDAY.00.PacBio.RSII_bax2bam.sh
@@ -8,7 +8,7 @@ source ./../../env.sh
 # set project-specific variables
 
 prefix="SK1.SMRTCell.1" # The file name prefix for the output files. For the testing example, run this script four times with the prefix of "SK1.SMRTCell.1", "SK1.SMRTCell.2", "SK1.SMRTCell.3", and "SK1.SMRTCell.4" respectively.
-pacbio_RSII_bax_fofn_file="./pacbio_fofn_files/SK1.SMRTCell.1.RSII_bax.fofn" # The fofn file containing file paths to the PacBio RSII bax reads from the same SMRT cell. If you have data from multiple SMRT cells, please run this script sepearately for each of them. Do not mix reads from different SMRT cells even though they come from the same sample. For the testing example, you can set pacbio_RSII_bax_fofn_file="./pacbio_fofn_files/$prefix.RSII_bax.fofn" to let this parameter to be automatically set up based on the prefix parameter.
+pacbio_RSII_bax_fofn_file="./pacbio_fofn_files/$prefix.RSII_bax.fofn" # The fofn file containing file paths to the PacBio RSII bax reads from the same SMRT cell. If you have data from multiple SMRT cells, please run this script sepearately for each of them. Do not mix reads from different SMRT cells even though they come from the same sample. For the testing example, you can set pacbio_RSII_bax_fofn_file="./pacbio_fofn_files/$prefix.RSII_bax.fofn" to let this parameter to be automatically set up based on the prefix parameter.
 
 #######################################
 # process the pipeline

diff --git a/Project_Template/00.Long_Reads/LRSDAY.00.Retrieve_Sample_PacBio_Reads.sh b/Project_Template/00.Long_Reads/LRSDAY.00.Retrieve_Sample_PacBio_Reads.sh
@@ -14,7 +14,7 @@ prefix="SK1" # The file name prefix for output files of the testing example.
 # process the pipeline
 
 echo "download the bam file from the ENA database ..."
-wget $file_url
+wget --no-check-certificate $file_url
 echo "bam2fastq ..."
 $bedtools_dir/bedtools bamtofastq -i $file_name -fq $prefix.filtered_subreads.fastq 
 echo "gzip fastq ..."
@@ -24,12 +24,12 @@ rm $file_name
 cd pacbio_fofn_files
 echo "download the metadata and raw PacBio reads in .h5 format ..."
 
-wget ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR108/ERR1080522/m150811_092723_00127_c100844062550000001823187612311514_s1_p0.metadata.xml
-wget ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR108/ERR1080529/m150813_110541_00127_c100823112550000001823177111031581_s1_p0.metadata.xml
-# wget ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR108/ERR1080536/m150814_201337_00127_c100823152550000001823177111031541_s1_p0.metadata.xml
-wget ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR108/ERR1080537/m150814_233250_00127_c100823152550000001823177111031542_s1_p0.metadata.xml
-# wget ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR1124245/m150910_184604_00127_c100822732550000001823176011031536_s1_p0.metadata.xml
-wget ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR114/ERR1140978/m150911_220012_00127_c100861772550000001823190702121671_s1_p0.metadata.xml
+wget --no-check-certificate ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR108/ERR1080522/m150811_092723_00127_c100844062550000001823187612311514_s1_p0.metadata.xml
+wget --no-check-certificate ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR108/ERR1080529/m150813_110541_00127_c100823112550000001823177111031581_s1_p0.metadata.xml
+# wget --no-check-certificate ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR108/ERR1080536/m150814_201337_00127_c100823152550000001823177111031541_s1_p0.metadata.xml
+wget --no-check-certificate ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR108/ERR1080537/m150814_233250_00127_c100823152550000001823177111031542_s1_p0.metadata.xml
+# wget --no-check-certificate ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR1124245/m150910_184604_00127_c100822732550000001823176011031536_s1_p0.metadata.xml
+wget --no-check-certificate ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR114/ERR1140978/m150911_220012_00127_c100861772550000001823190702121671_s1_p0.metadata.xml
 
 if [[ ! -d Analysis_Results ]]
 then
@@ -38,35 +38,35 @@ fi
 
 cd Analysis_Results
 
-wget ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR108/ERR1080522/m150811_092723_00127_c100844062550000001823187612311514_s1_p0.1.bax.h5
-wget ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR108/ERR1080522/m150811_092723_00127_c100844062550000001823187612311514_s1_p0.2.bax.h5
-wget ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR108/ERR1080522/m150811_092723_00127_c100844062550000001823187612311514_s1_p0.3.bax.h5
-wget ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR108/ERR1080522/m150811_092723_00127_c100844062550000001823187612311514_s1_p0.bas.h5
-
-wget ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR108/ERR1080529/m150813_110541_00127_c100823112550000001823177111031581_s1_p0.1.bax.h5
-wget ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR108/ERR1080529/m150813_110541_00127_c100823112550000001823177111031581_s1_p0.2.bax.h5
-wget ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR108/ERR1080529/m150813_110541_00127_c100823112550000001823177111031581_s1_p0.3.bax.h5
-wget ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR108/ERR1080529/m150813_110541_00127_c100823112550000001823177111031581_s1_p0.bas.h5
-
-# wget ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR108/ERR1080536/m150814_201337_00127_c100823152550000001823177111031541_s1_p0.1.bax.h5
-# wget ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR108/ERR1080536/m150814_201337_00127_c100823152550000001823177111031541_s1_p0.2.bax.h5
-# wget ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR108/ERR1080536/m150814_201337_00127_c100823152550000001823177111031541_s1_p0.3.bax.h5
-# wget ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR108/ERR1080536/m150814_201337_00127_c100823152550000001823177111031541_s1_p0.bas.h5
-
-wget ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR108/ERR1080537/m150814_233250_00127_c100823152550000001823177111031542_s1_p0.1.bax.h5
-wget ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR108/ERR1080537/m150814_233250_00127_c100823152550000001823177111031542_s1_p0.2.bax.h5
-wget ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR108/ERR1080537/m150814_233250_00127_c100823152550000001823177111031542_s1_p0.3.bax.h5
-wget ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR108/ERR1080537/m150814_233250_00127_c100823152550000001823177111031542_s1_p0.bas.h5
-
-# wget ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR1124245/m150910_184604_00127_c100822732550000001823176011031536_s1_p0.1.bax.h5
-# wget ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR1124245/m150910_184604_00127_c100822732550000001823176011031536_s1_p0.2.bax.h5
-# wget ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR1124245/m150910_184604_00127_c100822732550000001823176011031536_s1_p0.3.bax.h5
-# wget ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR1124245/m150910_184604_00127_c100822732550000001823176011031536_s1_p0.bas.h5
-
-wget ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR114/ERR1140978/m150911_220012_00127_c100861772550000001823190702121671_s1_p0.1.bax.h5
-wget ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR114/ERR1140978/m150911_220012_00127_c100861772550000001823190702121671_s1_p0.2.bax.h5
-wget ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR114/ERR1140978/m150911_220012_00127_c100861772550000001823190702121671_s1_p0.3.bax.h5
-wget ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR114/ERR1140978/m150911_220012_00127_c100861772550000001823190702121671_s1_p0.bas.h5
+wget --no-check-certificate ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR108/ERR1080522/m150811_092723_00127_c100844062550000001823187612311514_s1_p0.1.bax.h5
+wget --no-check-certificate ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR108/ERR1080522/m150811_092723_00127_c100844062550000001823187612311514_s1_p0.2.bax.h5
+wget --no-check-certificate ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR108/ERR1080522/m150811_092723_00127_c100844062550000001823187612311514_s1_p0.3.bax.h5
+wget --no-check-certificate ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR108/ERR1080522/m150811_092723_00127_c100844062550000001823187612311514_s1_p0.bas.h5
+
+wget --no-check-certificate ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR108/ERR1080529/m150813_110541_00127_c100823112550000001823177111031581_s1_p0.1.bax.h5
+wget --no-check-certificate ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR108/ERR1080529/m150813_110541_00127_c100823112550000001823177111031581_s1_p0.2.bax.h5
+wget --no-check-certificate ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR108/ERR1080529/m150813_110541_00127_c100823112550000001823177111031581_s1_p0.3.bax.h5
+wget --no-check-certificate ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR108/ERR1080529/m150813_110541_00127_c100823112550000001823177111031581_s1_p0.bas.h5
+
+# wget --no-check-certificate ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR108/ERR1080536/m150814_201337_00127_c100823152550000001823177111031541_s1_p0.1.bax.h5
+# wget --no-check-certificate ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR108/ERR1080536/m150814_201337_00127_c100823152550000001823177111031541_s1_p0.2.bax.h5
+# wget --no-check-certificate ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR108/ERR1080536/m150814_201337_00127_c100823152550000001823177111031541_s1_p0.3.bax.h5
+# wget --no-check-certificate ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR108/ERR1080536/m150814_201337_00127_c100823152550000001823177111031541_s1_p0.bas.h5
+
+wget --no-check-certificate ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR108/ERR1080537/m150814_233250_00127_c100823152550000001823177111031542_s1_p0.1.bax.h5
+wget --no-check-certificate ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR108/ERR1080537/m150814_233250_00127_c100823152550000001823177111031542_s1_p0.2.bax.h5
+wget --no-check-certificate ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR108/ERR1080537/m150814_233250_00127_c100823152550000001823177111031542_s1_p0.3.bax.h5
+wget --no-check-certificate ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR108/ERR1080537/m150814_233250_00127_c100823152550000001823177111031542_s1_p0.bas.h5
+
+# wget --no-check-certificate ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR1124245/m150910_184604_00127_c100822732550000001823176011031536_s1_p0.1.bax.h5
+# wget --no-check-certificate ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR1124245/m150910_184604_00127_c100822732550000001823176011031536_s1_p0.2.bax.h5
+# wget --no-check-certificate ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR1124245/m150910_184604_00127_c100822732550000001823176011031536_s1_p0.3.bax.h5
+# wget --no-check-certificate ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR112/ERR1124245/m150910_184604_00127_c100822732550000001823176011031536_s1_p0.bas.h5
+
+wget --no-check-certificate ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR114/ERR1140978/m150911_220012_00127_c100861772550000001823190702121671_s1_p0.1.bax.h5
+wget --no-check-certificate ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR114/ERR1140978/m150911_220012_00127_c100861772550000001823190702121671_s1_p0.2.bax.h5
+wget --no-check-certificate ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR114/ERR1140978/m150911_220012_00127_c100861772550000001823190702121671_s1_p0.3.bax.h5
+wget --no-check-certificate ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR114/ERR1140978/m150911_220012_00127_c100861772550000001823190702121671_s1_p0.bas.h5
 
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